PDB-8vj3: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from K...

ID or keywords:

Entry

Database: PDB / ID: 8vj3

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (FAD bound)

Components

Betaine aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Betaine aldehyde dehydrogenase (BetB)

Function / homology

Function and homology information

betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (FAD bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Jan 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vj3.cif.gz	766 KB	Display	PDBx/mmCIF format
PDB format	pdb8vj3.ent.gz	633.4 KB	Display	PDB format
PDBx/mmJSON format	8vj3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vj3_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8vj3_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8vj3_validation.xml.gz	76.9 KB	Display
Data in CIF	8vj3_validation.cif.gz	111.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/8vj3 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/8vj3	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Betaine aldehyde dehydrogenase

B: Betaine aldehyde dehydrogenase

C: Betaine aldehyde dehydrogenase

D: Betaine aldehyde dehydrogenase

hetero molecules

219 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	84.007, 100.789, 123.938
Angle α, β, γ (deg.)	90.00, 96.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Betaine aldehyde dehydrogenase Mass: 54062.281 Da / Num. of mol.: 4 / Mutation: V62A, Q485P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: betB_3 / Plasmid: KlaeA.00020.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A447LC14
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1138 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 5mM FAD soak ...Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 5mM FAD soak for 4 hours. 3 of the 4 subunits have disordered FAD in the nicotinamide ring so they appear as ADP. Plate 13676 well C10 drop 1. Puck: PSL-0803, Cryo: 30% PEG3350 + 70% crystallant.

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 49.02 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Berkeley C10: 100 mM Sodium acetate / Hydrochloric acid pH 4.5, 100 mM Ammonium phosphate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-Propanol, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. 5mM FAD soak ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9785 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.9→47.25 Å / Num. obs: 161437 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.046 / R_rim(I) all: 0.121 / Χ²: 0.99 / Net I/σ(I): 11.5 / Num. measured all: 1114981
Reflection shell	Resolution: 1.9→1.95 Å / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 1.145 / Num. measured all: 80872 / Num. unique obs: 11877 / CC_1/2: 0.717 / R_pim(I) all: 0.473 / R_rim(I) all: 1.241 / Χ²: 1.01 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5156: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→47.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1828	8140	5.04 %
R_work	0.157	-	-
obs	0.1583	161373	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→47.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14767	0	186	1138	16091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15526
X-RAY DIFFRACTION	f_angle_d	0.861	21152
X-RAY DIFFRACTION	f_dihedral_angle_d	13.15	5741
X-RAY DIFFRACTION	f_chiral_restr	0.053	2381
X-RAY DIFFRACTION	f_plane_restr	0.011	2759

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.92	0.2979	287	0.2713	5028	X-RAY DIFFRACTION	100
1.92-1.94	0.2866	239	0.2449	5110	X-RAY DIFFRACTION	100
1.94-1.97	0.2608	277	0.2339	5095	X-RAY DIFFRACTION	100
1.97-1.99	0.2672	262	0.2197	5090	X-RAY DIFFRACTION	100
1.99-2.02	0.2443	276	0.2101	5091	X-RAY DIFFRACTION	100
2.02-2.05	0.219	259	0.1983	5124	X-RAY DIFFRACTION	100
2.05-2.08	0.2436	273	0.1947	5098	X-RAY DIFFRACTION	100
2.08-2.11	0.2392	277	0.1895	5075	X-RAY DIFFRACTION	100
2.11-2.14	0.2375	275	0.1867	5062	X-RAY DIFFRACTION	100
2.14-2.17	0.2034	272	0.1932	5108	X-RAY DIFFRACTION	100
2.17-2.21	0.2284	288	0.1828	5090	X-RAY DIFFRACTION	100
2.21-2.25	0.208	278	0.1748	5084	X-RAY DIFFRACTION	100
2.25-2.3	0.212	275	0.1648	5081	X-RAY DIFFRACTION	100
2.3-2.34	0.1983	271	0.1591	5131	X-RAY DIFFRACTION	100
2.34-2.39	0.1948	274	0.1539	5076	X-RAY DIFFRACTION	100
2.39-2.45	0.19	267	0.1532	5084	X-RAY DIFFRACTION	100
2.45-2.51	0.187	247	0.152	5099	X-RAY DIFFRACTION	100
2.51-2.58	0.1983	276	0.1498	5142	X-RAY DIFFRACTION	100
2.58-2.65	0.1786	261	0.1569	5083	X-RAY DIFFRACTION	100
2.65-2.74	0.1879	261	0.1602	5135	X-RAY DIFFRACTION	100
2.74-2.84	0.2118	276	0.1753	5098	X-RAY DIFFRACTION	100
2.84-2.95	0.2104	273	0.169	5116	X-RAY DIFFRACTION	100
2.95-3.09	0.1934	259	0.1707	5128	X-RAY DIFFRACTION	100
3.09-3.25	0.192	254	0.1701	5133	X-RAY DIFFRACTION	100
3.25-3.45	0.1879	294	0.1666	5103	X-RAY DIFFRACTION	100
3.45-3.72	0.1764	293	0.1501	5102	X-RAY DIFFRACTION	100
3.72-4.09	0.1308	283	0.1266	5099	X-RAY DIFFRACTION	100
4.09-4.68	0.1156	264	0.1065	5148	X-RAY DIFFRACTION	100
4.68-5.9	0.157	286	0.1213	5169	X-RAY DIFFRACTION	100
5.9-47.25	0.1577	263	0.1519	5251	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.2938	0.0063	0.0199	1.0577	0.2638	0.2969	-0.0519	0.0146	-0.2423	-0.1631	-0.0201	-0.3114	0.1511	0.2994	-0.015	0.2024	0.0129	0.0173	0.2878	-0.0024	0.2729	93.2106	-13.639	19.6868
2	0.2978	0.3976	-0.1636	0.6461	0.0457	0.4046	-0.0189	0.0076	-0.0505	-0.0831	-0.0337	-0.0206	-0.0212	0.0423	-0	0.176	0.0112	-0.0265	0.1869	0.008	0.1886	81.1973	-5.9977	23.6751
3	0.7354	0.2648	-0.0018	0.7119	-0.2641	0.474	0.1109	-0.1255	0.2059	0.0783	-0.0482	-0.0774	-0.214	0.186	-0	0.309	-0.0476	0.0017	0.2331	0.0015	0.2663	86.857	20.3359	31.8612
4	0.4428	0.2702	-0.0205	0.1041	0.1151	0.3169	0.0368	0.0539	0.0743	-0.0005	-0.0196	0.0335	-0.0594	-0.0338	0	0.2273	0.0163	-0.009	0.1908	0.0189	0.2182	69.3624	5.5749	26.0556
5	0.2448	0.2508	0.0448	0.1619	0.0678	0.0325	-0.0253	0.1378	-0.07	-0.0093	-0.0539	0.5068	0.0589	-0.3362	-0	0.2201	-0.0096	0.031	0.3163	0.0261	0.4195	18.7159	-22.6413	45.8927
6	0.3384	-0.2839	0.0584	0.3555	0.2662	0.3497	-0.0468	0.2023	-0.121	-0.1093	0.0596	0.0953	0.1329	-0.1242	-0	0.2267	-0.0168	-0.0147	0.2434	-0.0346	0.2679	33.9518	-24.826	29.776
7	0.3668	-0.142	-0.2262	0.503	0.0244	0.2838	-0.0602	0.0096	-0.0399	0.0353	0.0479	0.0567	0.052	-0.0816	-0	0.1979	0.0036	-0.0174	0.2349	0.0023	0.2262	36.9949	-20.015	38.091
8	0.2624	0.2936	-0.1811	0.2404	0.2434	0.1772	0.039	-0.1097	-0.0032	0.0613	0.0196	-0.0609	-0.0089	0.1281	-0	0.2255	0.0362	0.0143	0.2557	-0.0031	0.2623	43.5629	-8.8909	53.5793
9	0.5723	0.0321	-0.0305	0.3632	0.2505	0.5438	0.0476	-0.188	0.1546	0.1815	-0.0315	0.1124	-0.0295	-0.0397	0	0.252	0.0101	0.0405	0.2711	-0.0307	0.2432	37.5196	0.8624	62.6884
10	0.4083	0.0081	-0.3853	0.2679	0.2339	0.4708	-0.015	-0.0366	-0.0519	0.0901	-0.0039	0.0681	0.0648	-0.0052	0	0.2294	0.0144	-0.0182	0.2118	0.0067	0.2119	54.6739	-14.3015	43.6269
11	0.1979	-0.177	-0.188	0.2725	0.126	0.2917	0.2185	0.4638	0.1988	-0.3847	-0.2355	0.2144	-0.4461	-0.4031	0.1177	0.4055	0.2773	-0.0132	0.5655	0.1608	0.2391	45.7056	4.0599	-6.6724
12	0.2862	-0.2202	-0.0548	0.4333	0.4327	0.3376	0.1812	0.0938	0.1932	0.1129	-0.0766	0.1288	-0.2797	-0.3249	0.0095	0.2452	0.0651	0.0095	0.2673	0.0264	0.2441	46.0684	2.2262	15.4089
13	0.6093	0.0131	-0.2114	0.24	0.2897	0.814	0.0924	0.2045	0.0014	-0.0224	-0.0534	-0.0075	-0.1026	-0.1982	0.0479	0.182	0.0524	-0.0225	0.2565	0.003	0.1652	51.6038	-4.5272	10.292
14	0.24	-0.3561	-0.1339	0.3655	0.2238	0.4864	-0.0376	0.1263	-0.0304	-0.0011	-0.0086	0.0207	0.0539	-0.0636	-0.0002	0.2607	-0.0155	-0.0162	0.3391	-0.0794	0.2391	61.2632	-19.7563	1.1241
15	0.0079	-0.1341	-0.1943	0.4607	0.1278	0.4323	-0.0637	0.3101	-0.1827	-0.2295	-0.003	0.031	0.0352	-0.4034	-0.0619	0.3017	-0.0279	-0.0236	0.4795	-0.1328	0.2396	55.1896	-26.9614	-13.4265
16	0.2047	0.0425	-0.3172	0.2277	0.0174	0.4849	-0.0504	0.2314	-0.1983	-0.0914	0.0071	-0.0626	0.1335	-0.1895	-0.0392	0.3089	-0.0052	0.0133	0.3754	-0.1319	0.2842	65.6802	-27.9907	-7.9258
17	0.2405	0.0853	-0.014	0.1037	0.1802	0.6028	-0.0344	0.0864	-0.062	-0.0737	-0.0129	-0.0148	-0.0289	-0.0399	-0	0.2112	-0.0031	-0.0072	0.2336	-0.0308	0.2234	64.3855	-17.5993	16.4445
18	0.5738	0.0674	0.2021	0.3504	0.2104	0.7467	-0.0837	-0.3135	-0.1756	0.1673	-0.0199	-0.1553	0.1395	0.1343	-0.0033	0.2839	0.0838	0.0141	0.3302	0.1006	0.2842	75.3042	-32.5756	56.4923
19	0.6023	0.0447	-0.0349	0.2203	-0.337	0.585	-0.0586	-0.2	-0.1908	0.0418	0.0063	-0.0241	0.1303	0.0109	-0.0101	0.2588	0.0383	0.0149	0.2357	0.0648	0.2689	64.0185	-31.1468	47.1891
20	0.1759	-0.0488	0.3295	0.2634	-0.3916	0.6129	-0.1143	-0.0258	-0.4303	-0.0027	0.0343	0.0401	0.5986	-0.0262	-0.138	0.6565	-0.0279	0.1245	0.2726	0.0261	0.5992	60.8937	-58.01	39.6397
21	0.2672	0.174	-0.1529	0.2181	-0.067	0.3431	-0.1171	-0.0327	-0.123	0.1137	0.0481	0.066	0.1518	-0.0556	-0.0029	0.2156	-0.0102	0.0143	0.1913	0.0086	0.2616	55.6151	-28.9661	35.2853

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 290 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 291 through 363 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 364 through 490 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 42 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 43 through 81 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 230 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 231 through 290 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 291 through 409 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 410 through 490 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 42 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 43 through 81 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 82 through 230 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 231 through 290 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 291 through 363 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 364 through 409 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 410 through 490 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 4 through 104 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 105 through 290 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 291 through 409 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 410 through 490 )

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